The Copenhagen Self-sampling Initiative (CSi) has shown how Human Papillomavirus (HPV)-based self-sampling can be used to increase screening participation among 23,632 non-attenders in Capital Region of Denmark. Here, we described the HPV prevalence and genotype frequency in 4824 self-samples using three HPV assays (CLART, Onclarity and HC2), and compared the results to the subsequent physician-taken follow-up samples. HPV self-sample findings were also compared to a reference population of routinely screened women (N=3347, from the Horizon study), undertaken in the same screening laboratory. Non-attenders had an HPV prevalence of 11.3% based on CLART, which was lower than women from Horizon (18.5%). One-third of the CSi women who tested HPV positive by self-sampling, were HPV negative in the subsequent physician-taken follow-up sample. CLART and Onclarity agreed in 64% (95%CI: 60-68%) of the HPV positive self-samples. Adding HC2 into a three-way comparison, the agreement decreased to 27% (95% CI: 24-29%). Our findings suggest that further validation of HPV assays for self-taken samples is needed for optimal HPV detection and correct clinical management of HPV positive women.